Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009633.1 Kokia drynarioides strain JFW-HI SEQ_124350, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 296665
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 48 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:233538 original size:59 final size:57
Alignment explanation
Indices: 233444--233595 Score: 177
Period size: 59 Copynumber: 2.6 Consensus size: 57
233434 CCAAAATTAC
*
233444 CATTTTAC-CCTCGAACATCTAAAATTACCATTTTACCCTTAAATGTCC-AAAAAT-T
1 CATTTTACTCC-CGAACATCCAAAATTACCATTTTACCCTTAAATGTCCAAAAAATAT
* * * *
233499 CCATTTTTGAC-CCCGAACTTTCCAAAAATTACCAATTTACCCTTAACTTTCCAAAAAATAT
1 -CA-TTTT-ACTCCCGAAC-ATCC-AAAATTACCATTTTACCCTTAAATGTCCAAAAAATAT
233560 CATTTTACTCCCGAACATCCAAAATTACCATTTTAC
1 CATTTTACTCCCGAACATCCAAAATTACCATTTTAC
233596 TCCCGAACAT
Statistics
Matches: 82, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
56 2 0.02
57 24 0.29
58 11 0.13
59 36 0.44
60 8 0.10
61 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (57 bp):
CATTTTACTCCCGAACATCCAAAATTACCATTTTACCCTTAAATGTCCAAAAAATAT
Found at i:233556 original size:30 final size:29
Alignment explanation
Indices: 233334--233826 Score: 186
Period size: 28 Copynumber: 17.1 Consensus size: 29
233324 CCTAAAAGGT
* * * *
233334 CCCTAAACTATCCAAAAATCA-TATTTTGA
1 CCCTTAACTTTCCAAAAATTACCATTTT-A
*
233363 CCCTCGAACTTTCCAAAAATTA-CATTTTAA
1 CCCT-TAACTTTCCAAAAATTACCATTTT-A
* * *
233393 CCCTCAAACTTTTC--AAATTTCCATTTTTGA
1 CCCT-TAACTTTCCAAAAATTACCA-TTTT-A
**
233423 CCCCAAACTTTCC-AAAATTACCATTTTA
1 CCCTTAACTTTCCAAAAATTACCATTTTA
* * *
233451 CCCTCGAAC-AT-CTAAAATTACCATTTTA
1 CCCT-TAACTTTCCAAAAATTACCATTTTA
* *
233479 CCCTTAAATGTCCAAAAATT-CCATTTTTGA
1 CCCTTAACTTTCCAAAAATTACCA-TTTT-A
** *
233509 CCCCGAACTTTCCAAAAATTACCAATTTA
1 CCCTTAACTTTCCAAAAATTACCATTTTA
* *
233538 CCCTTAACTTTCCAAAAAATATCATTTTA
1 CCCTTAACTTTCCAAAAATTACCATTTTA
** *
233567 CTCCCGAAC-ATCC-AAAATTACCATTTTA
1 C-CCTTAACTTTCCAAAAATTACCATTTTA
** *
233595 CTCCCGAAC-ATCC-AAAATTACCATTTTA
1 C-CCTTAACTTTCCAAAAATTACCATTTTA
* * * *
233623 CTCTCAGA-TGTT-TAATAATTA-CATTTTTTA
1 CCCTTA-ACT-TTCCAAAAATTACCA--TTTTA
** *
233653 CCCCAAACTTTTCAAAAATTACCATTTTA
1 CCCTTAACTTTCCAAAAATTACCATTTTA
** *
233682 CCCCTGGA-TGT-C-AAAATTA-CATTTTTTA
1 -CCCTTAACTTTCCAAAAATTACCA--TTTTA
* * * *
233710 -CCTCAAACTTTTCAAAAATTATCATTTTG
1 CCCT-TAACTTTCCAAAAATTACCATTTTA
** * * *
233739 CCCCCAAGTAT-AAAAAATTACCATTTTA
1 CCCTTAACTTTCCAAAAATTACCATTTTA
* *
233767 CCCCTAAC-ATCCAAAAATTACCATTTT-
1 CCCTTAACTTTCCAAAAATTACCATTTTA
* * * * *
233794 TCCTTGAGTGTCCAAAAATTACCGTTTTA
1 CCCTTAACTTTCCAAAAATTACCATTTTA
233823 CCCT
1 CCCT
233827 CGATCATCCC
Statistics
Matches: 361, Mismatches: 70, Indels: 66
0.73 0.14 0.13
Matches are distributed among these distances:
26 5 0.01
27 19 0.05
28 138 0.38
29 90 0.25
30 102 0.28
31 7 0.02
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTTAACTTTCCAAAAATTACCATTTTA
Found at i:233566 original size:29 final size:29
Alignment explanation
Indices: 233472--233567 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
233462 CTAAAATTAC
* *
233472 CATTTTACCCTTAAATGTCC-AAAAAT-T
1 CATTTTACCCTTAACTTTCCAAAAAATAT
** * *
233499 CCATTTTTGACCCCGAACTTTCCAAAAATTAC
1 -CA-TTTT-ACCCTTAACTTTCCAAAAAATAT
*
233531 CAATTTACCCTTAACTTTCCAAAAAATAT
1 CATTTTACCCTTAACTTTCCAAAAAATAT
233560 CATTTTAC
1 CATTTTAC
233568 TCCCGAACAT
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
28 2 0.04
29 30 0.58
30 13 0.25
31 7 0.13
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
CATTTTACCCTTAACTTTCCAAAAAATAT
Found at i:233612 original size:144 final size:144
Alignment explanation
Indices: 233344--233684 Score: 392
Period size: 144 Copynumber: 2.4 Consensus size: 144
233334 CCCTAAACTA
*
233344 TCCAAAAA-TCATATTTTGACCCTCGAACTTTCCAAAAATTA-CATTTTAACCCTCAAACTTTTC
1 TCCAAAAATTCAT-TTTTGACCC-CGAACTTTCCAAAAATTACCATTTT-ACCCTCAAACTTTCC
* * *
233407 AAATTTCCATTTTTGACCCCAAACTTTCCAAAATTACCATTTTACCCTCGAACATCTAAAATTAC
63 AAATATCCATTTTTGACCCCAAACTATCCAAAATTACCATTTTACCCTCGAACATCCAAAATTAC
*
233472 CATTTTACCCTTAAATG
128 CATTTTACCCTCAAATG
* *
233489 TCCAAAAATTCCATTTTTGACCCCGAACTTTCCAAAAATTACCAATTTACCCT-TAACTTTCCAA
1 TCCAAAAATT-CATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCAAACTTTCC--
*
233553 AAAATAT-CA-TTTT-ACTCCCGAAC-ATCCAAAATTACCATTTTACTCC-CGAACATCCAAAAT
63 -AAATATCCATTTTTGAC-CCCAAACTATCCAAAATTACCATTTTAC-CCTCGAACATCCAAAAT
* *
233613 TACCATTTTACTCTCAGATG
125 TACCATTTTACCCTCAAATG
** * * * *
233633 TTTAATAATTACATTTTTTACCCCAAACTTTTCAAAAATTACCATTTTACCC
1 TCCAAAAATT-CATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCC
233685 CTGGATGTCA
Statistics
Matches: 170, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
144 102 0.60
145 43 0.25
146 17 0.10
147 8 0.05
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (144 bp):
TCCAAAAATTCATTTTTGACCCCGAACTTTCCAAAAATTACCATTTTACCCTCAAACTTTCCAAA
TATCCATTTTTGACCCCAAACTATCCAAAATTACCATTTTACCCTCGAACATCCAAAATTACCAT
TTTACCCTCAAATG
Found at i:233683 original size:29 final size:29
Alignment explanation
Indices: 233369--233793 Score: 199
Period size: 28 Copynumber: 14.8 Consensus size: 29
233359 TTGACCCTCG
*
233369 AACTTTCCAAAAATTA-CATTTTAACCCTCA
1 AACTTTTCAAAAATTACCATTTT-ACCC-CA
*
233399 AACTTTTC--AAATTTCCATTTTTGACCCCA
1 AACTTTTCAAAAATTACCA-TTTT-ACCCCA
* *
233428 AAC-TTTCCAAAATTACCATTTTACCCTCG
1 AACTTTTCAAAAATTACCATTTTACCC-CA
* * *
233457 AAC--ATCTAAAATTACCATTTTACCCTTA
1 AACTTTTCAAAAATTACCATTTTACCC-CA
* * *
233485 AA-TGTCCAAAAATT-CCATTTTTGACCCCG
1 AACTTTTCAAAAATTACCA-TTTT-ACCCCA
* * **
233514 AACTTTCCAAAAATTACCAATTTACCCTT
1 AACTTTTCAAAAATTACCATTTTACCCCA
* * * *
233543 AACTTTCCAAAAAATATCATTTTACTCCCG
1 AACTTTTCAAAAATTACCATTTTAC-CCCA
* * *
233573 AAC--ATCCAAAATTACCATTTTACTCCCG
1 AACTTTTCAAAAATTACCATTTTAC-CCCA
* * *
233601 AAC--ATCCAAAATTACCATTTTACTCTCA
1 AACTTTTCAAAAATTACCATTTTAC-CCCA
* *
233629 GA-TGTTT-AATAATTA-CATTTTTTACCCCA
1 AACT-TTTCAAAAATTACCA--TTTTACCCCA
*
233658 AACTTTTCAAAAATTACCATTTTACCCCTG
1 AACTTTTCAAAAATTACCATTTTACCCC-A
* * *
233688 GA--TGTC-AAAATTA-CATTTTTTACCTCA
1 AACTTTTCAAAAATTACCA--TTTTACCCCA
* * *
233715 AACTTTTCAAAAATTATCATTTTGCCCCC
1 AACTTTTCAAAAATTACCATTTTACCCCA
* * * *
233744 AA-GTATAAAAAATTACCATTTTACCCCT
1 AACTTTTCAAAAATTACCATTTTACCCCA
* *
233772 AAC-ATCCAAAAATTACCATTTT
1 AACTTTTCAAAAATTACCATTTT
233794 TCCTTGAGTG
Statistics
Matches: 310, Mismatches: 57, Indels: 58
0.73 0.13 0.14
Matches are distributed among these distances:
26 2 0.01
27 8 0.03
28 136 0.44
29 88 0.28
30 69 0.22
31 7 0.02
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AACTTTTCAAAAATTACCATTTTACCCCA
Found at i:233717 original size:57 final size:60
Alignment explanation
Indices: 233608--233742 Score: 188
Period size: 57 Copynumber: 2.3 Consensus size: 60
233598 CCGAACATCC
* *
233608 AAAATTACCATTTTA-CTCTCAGATGTTTAATAATTACATTTTTTACCCCAAACTTTTCA
1 AAAATTACCATTTTACCCCTCAGATGTTCAATAATTACATTTTTTACCCCAAACTTTTCA
* *
233667 AAAATTACCATTTTACCCCT-GGATG-TCAA-AATTACATTTTTTACCTCAAACTTTTCA
1 AAAATTACCATTTTACCCCTCAGATGTTCAATAATTACATTTTTTACCCCAAACTTTTCA
* *
233724 AAAATTATCATTTTGCCCC
1 AAAATTACCATTTTACCCC
233743 CAAGTATAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
57 44 0.64
58 3 0.04
59 19 0.28
60 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (60 bp):
AAAATTACCATTTTACCCCTCAGATGTTCAATAATTACATTTTTTACCCCAAACTTTTCA
Found at i:233728 original size:144 final size:143
Alignment explanation
Indices: 233344--233794 Score: 382
Period size: 144 Copynumber: 3.1 Consensus size: 143
233334 CCCTAAACTA
* * * *
233344 TCCAAAAA-T-CATATTTTGACCCTCGAACTTTCCAAAAATTA-CATTTTAACCCTCAAACTTTT
1 TCCAAAAATTACAT-TTTTGACCC-CAAACTTTCCAAAAATTACCAATTT-ACCCT-GAAC-TGT
* * * *
233406 CAAATTTCCATTTTTGACCCCAAACTTTCCAAAATTACCATTTTACCCTCGAACATCTAAAATTA
61 CAAAATTACATTTTTTACCCCAAACTTTCCAAAATTACCATTTTACCCTCGAACATCCAAAATTA
*
233471 CCATTTTACCCTTAAATG
126 CCATTTTACCCTCAAATG
* * * *
233489 TCCAAAAATTCCATTTTTGACCCCGAACTTTCCAAAAATTACCAATTTACCCTTAACTTTCCAAA
1 TCCAAAAATTACATTTTTGACCCCAAACTTTCCAAAAATTACCAATTTACCCTGAACTGT-C-AA
* * *
233554 AAATATCA--TTTTACTCCCGAAC-ATCCAAAATTACCATTTTACTCC-CGAACATCCAAAATTA
64 AATTA-CATTTTTTAC-CCCAAACTTTCCAAAATTACCATTTTAC-CCTCGAACATCCAAAATTA
* *
233615 CCATTTTACTCTCAGATG
126 CCATTTTACCCTCAAATG
** * * * * *
233633 TTTAATAATTACATTTTTTACCCCAAACTTTTCAAAAATTACCATTTTACCCCTGGA-TGTCAAA
1 TCCAAAAATTACATTTTTGACCCCAAACTTTCCAAAAATTACCAATTTA-CCCTGAACTGTCAAA
* * * * * * **
233697 ATTACATTTTTTACCTCAAACTTTTCAAAAATTATCATTTTGCCC-CCAAGTATAAAAAATTACC
65 ATTACATTTTTTACCCCAAAC-TTTCCAAAATTACCATTTTACCCTCGAA-CATCCAAAATTACC
* **
233761 ATTTTACCC-CTAACA
128 ATTTTACCCTCAAATG
233776 TCCAAAAATTACCATTTTT
1 TCCAAAAATTA-CATTTTT
233795 CCTTGAGTGT
Statistics
Matches: 249, Mismatches: 42, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
141 2 0.01
142 11 0.04
143 25 0.10
144 143 0.57
145 48 0.19
146 17 0.07
147 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (143 bp):
TCCAAAAATTACATTTTTGACCCCAAACTTTCCAAAAATTACCAATTTACCCTGAACTGTCAAAA
TTACATTTTTTACCCCAAACTTTCCAAAATTACCATTTTACCCTCGAACATCCAAAATTACCATT
TTACCCTCAAATG
Found at i:233766 original size:57 final size:56
Alignment explanation
Indices: 233608--233793 Score: 155
Period size: 57 Copynumber: 3.2 Consensus size: 56
233598 CCGAACATCC
* * *
233608 AAAATTACCATTTTACTCTCA-GATGTTTAATAATTACATTTTTTACCCCAAACTTTTCA
1 AAAATTACCATTTTAC-CCCAGGATG--AAAAAATTACA-TTTTTACCCCAAACTTTTCA
* ** *
233667 AAAATTACCATTTTACCCCTGGATGTCAAAATTACATTTTTTACCTCAAACTTTTCA
1 AAAATTACCATTTTACCCCAGGATGAAAAAATTACA-TTTTTACCCCAAACTTTTCA
* * * * * *
233724 AAAATTATCATTTTGCCCCCAAGTAT-AAAAAATTACCA-TTTTACCCCTAAC-ATCCA
1 AAAATTACCATTTT-ACCCC-AGGATGAAAAAATTA-CATTTTTACCCCAAACTTTTCA
233780 AAAATTACCATTTT
1 AAAATTACCATTTT
233794 TCCTTGAGTG
Statistics
Matches: 107, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
56 16 0.15
57 53 0.50
58 13 0.12
59 25 0.23
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.38
Consensus pattern (56 bp):
AAAATTACCATTTTACCCCAGGATGAAAAAATTACATTTTTACCCCAAACTTTTCA
Found at i:233907 original size:28 final size:28
Alignment explanation
Indices: 233751--233927 Score: 115
Period size: 28 Copynumber: 6.2 Consensus size: 28
233741 CCCAAGTATA
* * *
233751 AAAAATTACCATTTTACCCCTAACATCC
1 AAAAATTACCATTTTGCCTCGAACATCC
* * ***
233779 AAAAATTACCATTTTTCCTTGAGTGTCC
1 AAAAATTACCATTTTGCCTCGAACATCC
* * *
233807 AAAAATTACCGTTTTACCCTCGATCATCC
1 AAAAATTACCATTTT-GCCTCGAACATCC
* * *
233836 CAAAATTACCATTTTGCCCCCGAGCAT-C
1 AAAAATTACCATTTTG-CCTCGAACATCC
* * * *
233864 TAAAATT-GCATTTTTGTCTCGAACTTCC
1 AAAAATTACCA-TTTTGCCTCGAACATCC
* **
233892 AAAAATTACCATTTTGCCCTTGGGCATCC
1 AAAAATTACCATTTTG-CCTCGAACATCC
233921 AAAAATT
1 AAAAATT
233928 GCATTTTTGA
Statistics
Matches: 112, Mismatches: 31, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
27 8 0.07
28 59 0.53
29 45 0.40
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (28 bp):
AAAAATTACCATTTTGCCTCGAACATCC
Found at i:236954 original size:17 final size:16
Alignment explanation
Indices: 236927--236958 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
236917 GTGGAGTAAA
236927 TTTGGTTGGTTGGTTC
1 TTTGGTTGGTTGGTTC
236943 TTTGGTTTGGTTGGTT
1 TTTGG-TTGGTTGGTT
236959 TGGATGACGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.03, G:0.38, T:0.59
Consensus pattern (16 bp):
TTTGGTTGGTTGGTTC
Found at i:238339 original size:6 final size:6
Alignment explanation
Indices: 238328--238362 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
238318 TATTTATGTA
238328 TAAAAT TAAAAT TAAAAT TAAAA- TAATAAT TAAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAA-AAT TAAAA
238363 CCAAATCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 3 0.11
6 21 0.78
7 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAAAT
Found at i:239818 original size:22 final size:22
Alignment explanation
Indices: 239776--239818 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
239766 TTGATTTAAT
*
239776 TATCTAAAAATTACACTTTTAC
1 TATCTAAAAATTACACATTTAC
239798 TATCATAAAAATTACA-ATTTA
1 TATC-TAAAAATTACACATTTA
239819 ATTTTAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (22 bp):
TATCTAAAAATTACACATTTAC
Found at i:242680 original size:28 final size:28
Alignment explanation
Indices: 242586--242680 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 28
242576 AGTATATTGT
* * *
242586 CAATCACTCAACTTTTATTAAAATAGCAAAA
1 CAATCACTAAAC-TTTA--AAAATAACAAAC
* * *
242617 CAATCACTAAATTTTGAAAAATTA-TAAC
1 CAATCACTAAACTTT-AAAAATAACAAAC
*
242645 TCAGTCACTAAACTTTAAAAATAACAAAC
1 -CAATCACTAAACTTTAAAAATAACAAAC
242674 CAATCAC
1 CAATCAC
242681 CGGTAATCAT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
28 15 0.30
29 21 0.42
30 3 0.06
31 11 0.22
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.27
Consensus pattern (28 bp):
CAATCACTAAACTTTAAAAATAACAAAC
Found at i:243803 original size:29 final size:30
Alignment explanation
Indices: 243732--243803 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
243722 ATGATAGTGG
* * *
243732 GTGACTGATTTGTTATTTTTCTAAAGTTTA
1 GTGACTGATTTGTAACTTTTCTAAAATTTA
* *
243762 GTGATTGAGTTGTAACTTTT-TAAAATTTA
1 GTGACTGATTTGTAACTTTTCTAAAATTTA
*
243791 GTGACTGTTTTGT
1 GTGACTGATTTGT
243804 TATTTCCATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.24, C:0.06, G:0.19, T:0.51
Consensus pattern (30 bp):
GTGACTGATTTGTAACTTTTCTAAAATTTA
Found at i:244705 original size:31 final size:32
Alignment explanation
Indices: 244658--244728 Score: 108
Period size: 31 Copynumber: 2.2 Consensus size: 32
244648 AGATTTCAAT
244658 AACATAATTTTTTTGTTATAAATTTATAAAATA
1 AACATAA-TTTTTTGTTATAAATTTATAAAATA
*
244691 AACATAA-TTTTTGTTATAACTTTATAAAATA
1 AACATAATTTTTTGTTATAAATTTATAAAATA
*
244722 CACATAA
1 AACATAA
244729 ATTCTTAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 29 0.81
33 7 0.19
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (32 bp):
AACATAATTTTTTGTTATAAATTTATAAAATA
Found at i:248585 original size:11 final size:10
Alignment explanation
Indices: 248550--248601 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
248540 TTTTAAAAAA
*
248550 TAAAAGTTAT
1 TAAAAATTAT
*
248560 T-AAATTTATT
1 TAAAAATTA-T
248570 TAAAAATTAT
1 TAAAAATTAT
248580 TAAAAATATAT
1 TAAAAAT-TAT
*
248591 AAAAAATTAT
1 TAAAAATTAT
248601 T
1 T
248602 TTTTAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 6 0.17
10 14 0.40
11 15 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:248593 original size:20 final size:20
Alignment explanation
Indices: 248549--248601 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
248539 ATTTTAAAAA
* **
248549 ATAAAAGTTATTAAATTTAT
1 ATAAAAATTATTAAAAATAT
*
248569 TTAAAAATTATTAAAAATAT
1 ATAAAAATTATTAAAAATAT
248589 ATAAAAAATTATT
1 AT-AAAAATTATT
248602 TTTTAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAAAAATTATTAAAAATAT
Found at i:248607 original size:35 final size:34
Alignment explanation
Indices: 248524--248618 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 34
248514 ATTAATAATT
* *
248524 AATTATTTTTTTAAAATT-TTAAAAAATAAAAGT
1 AATTATTTTTTAAAAATTATTAAAAAATAAAAGA
*
248557 TATTAAATTTATTTAAAAATTATTAAAAATATATAAA-A
1 AATT--ATTT-TTTAAAAATTATTAAAAA-ATA-AAAGA
248595 AATTATTTTTTAAAAATTAATTAA
1 AATTATTTTTTAAAAATT-ATTAA
248619 TTGTTAACGT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
33 3 0.06
35 14 0.27
36 18 0.35
37 7 0.14
38 6 0.12
39 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (34 bp):
AATTATTTTTTAAAAATTATTAAAAAATAAAAGA
Found at i:250951 original size:18 final size:18
Alignment explanation
Indices: 250912--250964 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
250902 TTGTTTATAT
* *
250912 ATATTTA-AAATATTAAA
1 ATATTTATAAAAATAAAA
250929 A-ATTTATAAAAATAAAA
1 ATATTTATAAAAATAAAA
250946 ATATTT-TAAAAAATAAAA
1 ATATTTAT-AAAAATAAAA
250964 A
1 A
250965 AATTGTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 5 0.16
17 11 0.35
18 15 0.48
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATTTATAAAAATAAAA
Found at i:252678 original size:19 final size:19
Alignment explanation
Indices: 252620--252680 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
252610 AAGTAAACTA
252620 TCAAAGTCAACGA-TCAAGG
1 TCAAAGTCAACGAGTC-AGG
* * * *
252639 TAAAAGTCAATGGGTCTGG
1 TCAAAGTCAACGAGTCAGG
*
252658 TCAAAGTCAACAAGTCAGG
1 TCAAAGTCAACGAGTCAGG
252677 TCAA
1 TCAA
252681 CAGTTCGGCC
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 30 0.94
20 2 0.06
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (19 bp):
TCAAAGTCAACGAGTCAGG
Found at i:254388 original size:3 final size:3
Alignment explanation
Indices: 254375--254403 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
254365 CTTTATTTAT
254375 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
254404 CACAATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:256920 original size:19 final size:19
Alignment explanation
Indices: 256898--256940 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
256888 AACGATCAAT
* **
256898 GTCAATGTCAACGGGTCTG
1 GTCAAAGTCAACAAGTCTG
256917 GTCAAAGTCAACAAGTCTG
1 GTCAAAGTCAACAAGTCTG
256936 GTCAA
1 GTCAA
256941 CGATTTGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (19 bp):
GTCAAAGTCAACAAGTCTG
Found at i:256995 original size:27 final size:27
Alignment explanation
Indices: 256951--257015 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
256941 CGATTTGGTT
*
256951 AACTCGGGTCAATAGGTCAAGTCAGTC
1 AACTCGGGTCAACAGGTCAAGTCAGTC
* * ** *
256978 AACTCGGGTCAACGGGTCAGGTTGGTT
1 AACTCGGGTCAACAGGTCAAGTCAGTC
257005 AACTCGGGTCA
1 AACTCGGGTCA
257016 CATGCGGGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.23
Consensus pattern (27 bp):
AACTCGGGTCAACAGGTCAAGTCAGTC
Found at i:272393 original size:31 final size:30
Alignment explanation
Indices: 272357--272463 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 30
272347 CATTTGAGAA
*
272357 ACCCTTATTTGAGCACTTTTGAAAATGTTTG
1 ACCCTTATTTGAGCA-TTTTGAAAAGGTTTG
* *
272388 ACCCTTATTTGAGCATTGTCGAAAAGGTTAG
1 ACCCTTATTTGAGCATT-TTGAAAAGGTTTG
* * * *
272419 GCCCTTATTCGATCATTTTG-TAAGGTTT-
1 ACCCTTATTTGAGCATTTTGAAAAGGTTTG
272447 ACCCTTCAATTTGAGCA
1 ACCCTT--ATTTGAGCA
272464 CTTCTTATGT
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
28 5 0.08
29 6 0.10
30 11 0.18
31 39 0.64
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (30 bp):
ACCCTTATTTGAGCATTTTGAAAAGGTTTG
Found at i:272771 original size:18 final size:18
Alignment explanation
Indices: 272745--272780 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
272735 AGTTGTCACG
*
272745 TCAATAAATTTTAAAAAT
1 TCAAAAAATTTTAAAAAT
272763 TCAAAAAATTTTAAAAAT
1 TCAAAAAATTTTAAAAAT
272781 AAGAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
TCAAAAAATTTTAAAAAT
Found at i:272954 original size:21 final size:19
Alignment explanation
Indices: 272908--272955 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
272898 TTTTTTTTTT
*
272908 ATAAATTTGTAAAATATTA
1 ATAAATTTATAAAATATTA
*
272927 TTAAAATTTATAAAAATATTAA
1 AT-AAATTTAT-AAAATATT-A
272949 ATAAATT
1 ATAAATT
272956 CAAAATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 7 0.30
21 13 0.57
22 2 0.09
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAAATTTATAAAATATTA
Found at i:282805 original size:13 final size:13
Alignment explanation
Indices: 282789--282826 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
282779 AGGAATATAA
282789 ATAGGAAATAAAT
1 ATAGGAAATAAAT
282802 ATAGGAAATACAAT
1 ATAGGAAATA-AAT
282816 A-AGGAAA-AAAT
1 ATAGGAAATAAAT
282827 TATAAAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.12
12 1 0.04
13 16 0.67
14 4 0.17
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (13 bp):
ATAGGAAATAAAT
Found at i:282830 original size:26 final size:25
Alignment explanation
Indices: 282778--282826 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
282768 ATTAATTAAT
282778 TAGGAATATAAATAGGAAATAAATA
1 TAGGAATATAAATAGGAAATAAATA
282803 TAGGAA-ATACAATAAGGAAA-AAAT
1 TAGGAATATA-AAT-AGGAAATAAAT
282827 TATAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.61, C:0.02, G:0.16, T:0.20
Consensus pattern (25 bp):
TAGGAATATAAATAGGAAATAAATA
Found at i:282962 original size:21 final size:21
Alignment explanation
Indices: 282894--282975 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 21
282884 TATGGCATGC
282894 AAATAAAT-ATAATATCAATAA-
1 AAATAAATAATAA-AT-AATAAT
* *
282915 AATTAAATATTATAAAATAACACAT
1 AAATAAATA--AT-AAATAATA-AT
282940 AAATAAATAATAAATAATAAT
1 AAATAAATAATAAATAATAAT
*
282961 AAATCAAAAAATAAA
1 AAAT-AAATAATAAA
282976 CAAACAATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
21 13 0.27
22 16 0.33
23 5 0.10
24 5 0.10
25 10 0.20
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAATAATAAATAATAAT
Found at i:292196 original size:59 final size:60
Alignment explanation
Indices: 292082--292196 Score: 205
Period size: 60 Copynumber: 1.9 Consensus size: 60
292072 CTTCATCTTC
*
292082 TTCACGGTAAAACAAGAGAAGAACTAGGGTTTTCCATTGTTAACTTTTGAAGCTTGCTTT
1 TTCAAGGTAAAACAAGAGAAGAACTAGGGTTTTCCATTGTTAACTTTTGAAGCTTGCTTT
*
292142 TTCAAGGTAATACAAGAGAAGAACTAGGG-TTTCCATTGTTAACTTTTGAAGCTTG
1 TTCAAGGTAAAACAAGAGAAGAACTAGGGTTTTCCATTGTTAACTTTTGAAGCTTG
292197 ATTAGGTGAG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
59 26 0.49
60 27 0.51
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (60 bp):
TTCAAGGTAAAACAAGAGAAGAACTAGGGTTTTCCATTGTTAACTTTTGAAGCTTGCTTT
Done.